Metal Binding and Selectivity in Zinc Proteins

Chemistry meets biology in the coordination dynamics of metalloproteins

Metal sites in proteins are often presented in an idealized way that does not capture the intrinsic dynamic behavior of the protein or the extrinsic factors that affect changes in the coordination of the metal ion in biological space and time. The bioinorganic chemistry possible in healthy and diseased living organisms is limited by prevailing pH values, redox potentials, and availability and concentrations of metal ions and ligands. Changes in any of these parameters and protein-protein or protein-ligand interactions can result in differences in the type of metal ion bound, metal occupancy, and coordination number or geometry. This article addresses the plasticity and complexity of metal coordination in proteins when these parameters are considered. It uses three examples of zinc sites with sulfur donor atoms from cysteines in mammalian proteins: alcohol dehydrogenases, metallothioneins, and zinc transporters of the ZnT (SLC30A) family. Coordination dynamics of the metal sites in these proteins has different purposes; in alcohol dehydrogenases for the metal ion to perform its different roles in the catalytic cycle, in metallothioneins for serving as a metal buffer, and in ZnT zinc transporters for sensing metal ions and moving them through the protein and thus biological membranes. Defining the biological and chemical parameters that determine and affect coordination dynamics of metal ions in proteins will inform future investigations of metalloproteins.

From quantum-derived principles underlying cysteine reactivity to combating the COVID-19 pandemic

The COVID-19 pandemic poses a challenge in coming up with quick and effective means to counter its cause, the SARS-CoV-2. Here, we show how the key factors governing cysteine reactivity in proteins derived from combined quantum mechanical/continuum calculations led to a novel multi-targeting strategy against SARS-CoV-2, in contrast to developing potent drugs/vaccines against a single viral target such as the spike protein. Specifically, they led to the discovery of reactive cysteines in evolutionary conserved Zn2+-sites in several SARS-CoV-2 proteins that are crucial for viral polypeptide proteolysis as well as viral RNA synthesis, proofreading, and modification. These conserved, reactive cysteines, both free and Zn2+-bound, can be targeted using the same Zn-ejector drug (disulfiram/ebselen), which enables the use of broad-spectrum anti-virals that would otherwise be removed by the virus's proofreading mechanism. Our strategy of targeting multiple, conserved viral proteins that operate at different stages of the virus life cycle using a Zn-ejector drug combined with other broad-spectrum anti-viral drug(s) could enhance the barrier to drug resistance and antiviral effects, as compared to each drug alone. Since these functionally important nonstructural proteins containing reactive cysteines are highly conserved among coronaviruses, our proposed strategy has the potential to tackle future coronaviruses. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisStructure and Mechanism > Computational Biochemistry and BiophysicsElectronic Structure Theory > Density Functional Theory.

How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins

The results obtained reveal that applying mechanical forces with a given strength and directionality can modulate the metal affinity and selectivity of metal binding sites in metalloproteins.

Bioinformatic Exploration of Metal-Binding Proteome of Zoonotic Pathogen Orientia tsutsugamushi

Metal ions are involved in many essential biological processes and are crucial for the survival of all organisms. Identification of metal-binding proteins (MBPs) of human affecting pathogens may provide the blueprint for understanding biological metal usage and their putative roles in pathogenesis. This study is focused on the analysis of MBPs from Orientia tsutsugamushi (Ott), a causal agent of scrub typhus in humans. A total of 321 proteins were predicted as putative MBPs, based on sequence search and three-dimensional structure analysis. Majority of proteins could bind with magnesium, and the order of metal binding was Mg > Ca > Zn > Mn > Fe > Cd > Ni > Co > Cu, respectively. The predicted MBPs were functionally classified into nine broad classes. Among them, gene expression and regulation, metabolism, cell signaling, and transport classes were dominant. It was noted that the putative MBPs were localized in all subcellular compartments of Ott, but majorly found in the cytoplasm. Additionally, it was revealed that out of 321 predicted MBPs 245 proteins were putative bacterial toxins and among them, 98 proteins were nonhomologous to human proteome. Sixty putative MBPs showed the ability to interact with drug or drug-like molecules, which indicate that they may be used as broad-spectrum drug targets. These predicted MBPs from Ott could play vital role(s) in various cellular activities and virulence, hence may serve as plausible therapeutic targets to design metal-based drugs to curtail its infection.

The potential use of natural vs commercial biosorbent material to remediate stream waters by removing heavy metal contaminants

The presence of high level of heavy metals in aquatic environment is a cause of ecological and environmental concern and thus their removal from water courses is environmentally essential. Four natural inexpensive biosorbents: macro algae (Fucus vesiculosus), crab shells (Cancer pagurus), wood chippings and iron-rich soil were tested for copper (Cu²⁺) and zinc (Zn²⁺) removal from aqueous solutions. Batch equilibrations were performed at 1:100 w/v with different initial metal concentrations. Three macro algae pre-treatments (unmodified (UM algae), chemically treated (Ca-T algae) and thermally treated (T-T algae)) were additionally investigated for performance. The sorption capacities were compared with the commercial material biochar and activated carbon. The maximum level of the sorbents for Cu²⁺ uptake at 15.7 mM/l was attained by the natural material of UM algae (72.37 ± 0.37 mg/g) > Ca-T algae (66.77 ± 0.19 mg/g) > T-T algae (63.06 ± 0.82 mg/g), followed by the commercial material activated carbon (36.71 ± 2.20 mg/g). The maximum level of the sorbents for Zn²⁺ uptake at 15.3 mM/l was also achieved by the natural material of UM algae (52.40 ± 0.80 mg/g) > Ca-T algae (48.83 ± 2.01 mg/g) > T-T algae (39.57 ± 0.80 mg/g) followed by the commercial material activated carbon (20.78 ± 1.63 mg/g) and biochar (18.07 ± 1.09 mg/g). The results demonstrated that Cu²⁺ and Zn²⁺ were effectively removed by these biosorbents at all concentrations. However, at high metals concentrations, the natural material macro algae had greater Cu²⁺ and Zn²⁺ sorption capacity than the conventional sorbent activated carbon, and the affinity of these natural biosorbents were greater for Cu²⁺ than Zn²⁺. Hence, inexpensive natural and readily available materials showed potential as biosorbents to remediate polluted stream water of toxic metal contaminants.

Development of METAL-ACTIVE SITE and ZINCCLUSTER tool to predict active site pockets

The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in Protein Data Bank, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions. User can also gain information about the residues present in the first and second coordination sphere as it plays a major role in maintaining the structure and function of metalloproteins in biological system. In this paper, a novel computational tool (ZINCCLUSTER) is developed, which can predict the zinc metal binding sites of proteins even if only the primary sequence is known. The purpose of this tool is to predict the active site cluster of an uncharacterized protein based on its primary sequence or a 3D structure. The tool can predict amino acids interacting with a metal or vice versa. This tool is based on the occurrence of significant triplets and it is tested to have higher prediction accuracy when compared to that of other available techniques.

An efficient protocol for computing the pKa of Zn-bound water

We present an efficient and accurate method for computing absolute pK_w values in Zn²⁺ complexes.

Spectroscopic Studies of the EutT Adenosyltransferase from Salmonella enterica: Evidence of a Tetrahedrally Coordinated Divalent Transition Metal Cofactor with Cysteine Ligation

The EutT enzyme from Salmonella enterica, a member of the family of ATP:cobalt(I) corrinoid adenosyltransferase (ACAT) enzymes, requires a divalent transition metal ion for catalysis, with Fe(II) yielding the highest activity. EutT contains a unique cysteine-rich HX₁₁CCX₂C(83) motif (where H and the last C occupy the 67th and 83rd positions, respectively, in the amino acid sequence) not found in other ACATs and employs an unprecedented mechanism for the formation of adenosylcobalamin. Recent kinetic and spectroscopic studies of this enzyme revealed that residues in the HX₁₁CCX₂C(83) motif are required for the tight binding of the divalent metal ion and are critical for the formation of a four-coordinate (4c) cob(II)alamin [Co(II)Cbl] intermediate in the catalytic cycle. However, it remained unknown which, if any, of the residues in the HX₁₁CCX₂C(83) motif bind the divalent metal ion. To address this issue, we have characterized Co(II)-substituted wild-type EutT (EutT^WT/Co) by using electronic absorption, electron paramagnetic resonance, and magnetic circular dichroism (MCD) spectroscopies. Our results indicate that the reduced catalytic activity of EutT^WT/Co relative to that of the Fe(II)-containing enzyme arises from the incomplete incorporation of Co(II) ions and, thus, a decrease in the relative population of 4c Co(II)Cbl. Our MCD data for EutT^WT/Co also reveal that the Co(II) ions reside in a distorted tetrahedral coordination environment with direct cysteine sulfur ligation. Additional spectroscopic studies of EutT/Co variants possessing a single alanine substitution of either His67, His75, Cys79, Cys80, or Cys83 indicate that Cys80 coordinates to the Co(II) ion, while the additional residues are important for maintaining the structural integrity and/or high affinity of the metal binding site.

Bioinformatics survey of the metal usage by psychrophilic yeast Glaciozyma antarctica PI12

Metal ions are one of the essential elements which are extensively involved in many cellular activities. With rapid advancements in genome sequencing techniques, bioinformatics approaches have provided a promising way to extract functional information of a protein directly from its primary structure. Recent findings have suggested that the metal content of an organism can be predicted from its complete genome sequences. Characterizing the biological metal usage of cold-adapted organisms may help to outline a comprehensive understanding of the metal-partnerships between the psychrophile and its adjacent environment. The focus of this study is targeted towards the analysis of the metal composition of a psychrophilic yeast Glaciozyma antarctica PI12 isolated from sea ice of Antarctica. Since the cellular metal content of an organism is usually reflected in the expressed metal-binding proteins, the putative metal-binding sequences from G. antarctica PI12 were identified with respect to their sequence homologies, domain compositions, protein families and cellular distribution. Most of the analyses revealed that the proteome was enriched with zinc, and the content of metal decreased in the order of Zn > Fe > Mg > Mn, Ca > Cu. Upon comparison, it was found that the metal compositions among yeasts were almost identical. These observations suggested that G. antarctica PI12 could have inherited a conserved trend of metal usage similar to modern eukaryotes, despite its geographically isolated habitat.

The dynamics of zinc sites in proteins: electronic basis for coordination sphere expansion at structural sites

The functional role assumed by zinc in proteins is closely tied to the variable dynamics around its coordination sphere arising by virtue of its flexibility in bonding. Modern experimental and computational methods allow the detection and study of previously unknown features of bonding between zinc and its ligands in protein environment. These discoveries are occurring just in time as novel biological functions of zinc, which involve rather unconventional coordination trends, are emerging. In this sense coordination sphere expansion of structural zinc sites, as observed in our previous experiments, is a novel phenomenon. Here we explore the electronic and structural requirements by simulating this phenomenon in structural zinc sites using DFT computations. For this purpose, we have chosen MPW1PW91 and a mixed basis set combination as the DFT method through benchmarking, because it accurately reproduces structural parameters of experimentally characterized zinc compounds. Using appropriate models, we show that the greater ionic character of zinc coordination would allow for coordination sphere expansion if the steric and electrostatic repulsions of the ligands are attenuated properly. Importantly, through the study of electronic and structural aspects of the models used, we arrive at a comprehensive bonding model, explaining the factors that influence coordination of zinc in proteins. The proposed model along with the existing knowledge would enhance our ability to predict zinc binding sites in proteins, which is today of growing importance given the predicted enormity of the zinc proteome.

Competition among Ca2+, Mg2+, and Na+ for model ion channel selectivity filters: determinants of ion selectivity

Because voltage-gated ion channels play critical biological roles, understanding how they can discriminate the native metal ion from rival cations in the milieu is of great interest. Although Ca(2+), Mg(2+), and Na(+) are present in comparable concentrations outside the cell, the factors governing the competition among these cations for the selectivity filter of voltage-gated Ca(2+) ion channel remain unclear. Using density functional theory combined with continuum dielectric methods, we evaluate the effect of (1) the number, chemical type, and charge of the ligands lining the pore, (2) the pore's rigidity, size, symmetry, and solvent accessibility, and (3) the Ca(2+) hydration number outside the selectivity filter on the competition among Ca(2+), Mg(2+), and Na(+) in model selectivity filters. The calculations show how the outcome of this competition depends on the interplay between electronic and solvation effects. Selectivity for monovalent Na(+) over divalent Ca(2+)/Mg(2+) is achieved when solvation effects outweigh electrostatic effects; thus filters comprising a few weak charge-donating groups such as Ser/Thr side chains, where electrostatic effects are relatively weak and are easily overcome by solvation effects, are Na(+)-selective. In contrast, selectivity for divalent Ca(2+)/Mg(2+) over monovalent Na(+) is achieved when metal-ligand electrostatic effects outweigh solvation effects. The key differences in selectivity between Mg(2+) and Ca(2+) lie in the pore size, oligomericity, and solvent accessibility. The results, which are consistent with available experimental data, reveal how the structure and composition of the ion channel selectivity pore had adapted to the specific physicochemical properties of the native metal ion to enhance the competitiveness of the native metal toward rival cations.

Metal binding affinity and selectivity in metalloproteins: insights from computational studies

This review highlights insights gained from computational studies on protein-metal recognition. We systematically dissect the various factors governing metal binding affinity and selectivity in proteins starting from (a) the intrinsic properties of the metal and neighboring metal cations (if present), to (b) the primary coordination sphere, (c) the second coordination shell, (d) the protein matrix, (e) the bulk solvent, and (f) competing non-protein ligands from the surrounding biological environment. The results herein reveal the fundamental principles and the molecular bases underlying protein-metal recognition, which serve as a guide to engineer novel metalloproteins with programmed properties.

Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus

The chemical properties of zinc make it an ideal metal to study the role of coordination strain in enzymatic rate enhancement. The zinc ion and the protein residues that are bound directly to the zinc ion represent a functional charge/dipole complex, and polarization of this complex, which translates to coordination distortion, may tune electrophilicity, and hence, reactivity. Conserved protein residues outside of the charge/dipole complex, such as second-shell residues, may play a role in supporting the electronic strain produced as a consequence of functional polarization. To test the correlation between charge/dipole polarity and ligand binding affinity, structure-function studies were carried out on the dizinc aminopeptidase from Vibrio proteolyticus. Alanine substitutions of S228 and M180 resulted in catalytically diminished enzymes whose crystal structures show very little change in the positions of the metal ions and the protein residues. However, more detailed inspections of the crystal structures show small positional changes that account for differences in the zinc ion coordination geometry. Measurements of the binding affinity of leucine phosphonic acid, a transition state analogue, and leucine, a product, show a correlation between coordination geometry and ligand binding affinity. These results suggest that the coordination number and polarity may tune the electrophilicity of zinc. This may have provided the evolving enzyme with the ability to discriminate between reaction coordinate species.

Effect of carboxylate-binding mode on metal binding/selectivity and function in proteins

We delineate the factors governing the carboxylate-binding mode (monodentate vs bidentate) in metalloproteins. We reveal how the carboxylate-binding mode affects the binding affinity and selectivity of a metal ion as well as the function of a metalloprotein using Ca2+-binding proteins and enzymes (ribonuclease H1, phosphoserine phosphatase, and ribonucleotide reductase) as examples. The collected data indicate that a carboxylate monodentate left arrow over right arrow bidentate switch, in addition to other structural factors, could be used to fine tune the metal-binding site affinity and/or selectivity, thus modifying the function/properties of the metalloprotein.

Zn protein simulations including charge transfer and local polarization effects

Nearly half of all proteins contain metal ions, which perform a wide variety of specific functions associated with life processes. However, insights into the local/global, structural and dynamical fluctuations in metalloproteins from molecular dynamics simulations have been hampered by the "conventional" potential energy function (PEF) used in nonmetalloprotein simulations, which does not take into the nonnegligible charge transfer and polarization effects in many metal complexes. Here, we have carried out molecular dynamics simulations of Zn(2+) bound to Cys(-) and/or His(0) in proteins using both the conventional PEF and a novel PEF that accounts for the significant charge transfer and polarization effects in these Zn complexes. Simulations with the conventional PEF yield a nontetrahedral Cys(2)His(2) Zn-binding site and significantly overestimate the experimental Zn-S(Cys(-)) distance. In contrast, simulations with the new PEF accurately reproduce the experimentally observed tetrahedral structures of Cys(2)His(2) and Cys(4) Zn-binding sites in proteins, even when the simulation started from a nontetrahedral Zn(2+) configuration. This suggests that simulations with the new PEF could account for coordinational changes at Zn, which occurs during the folding/unfolding of Zn-finger proteins and certain enzymatic reactions The strategy introduced here can easily be applied to investigate Zn(2+) interacting with protein ligands other than Cys(-) and His(0). It can also be extended to study the interaction of other metals that have significant charge transfer and polarization effects.